Zinc in PDB 6aze: Crystal Structure of the Bptf Phd-Bromodomain Module Bound to H3KC4ME3 Methyl Lysine Analog

The structure of Crystal Structure of the Bptf Phd-Bromodomain Module Bound to H3KC4ME3 Methyl Lysine Analog, PDB code: 6aze was solved by Z.Chen, A.J.Ruthenburg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.62 / 2.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.263, 64.130, 85.670, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 21.3

The binding sites of Zinc atom in the Crystal Structure of the Bptf Phd-Bromodomain Module Bound to H3KC4ME3 Methyl Lysine Analog (pdb code 6aze). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Bptf Phd-Bromodomain Module Bound to H3KC4ME3 Methyl Lysine Analog, PDB code: 6aze:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Bptf Phd-Bromodomain Module Bound to H3KC4ME3 Methyl Lysine Analog


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Bptf Phd-Bromodomain Module Bound to H3KC4ME3 Methyl Lysine Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:20.8 occ:1.00 ND1 A:HIS34 2.0 23.1 1.0 SG A:CYS37 2.3 20.1 1.0 SG A:CYS13 2.4 25.2 1.0 SG A:CYS11 2.4 20.1 1.0 CE1 A:HIS34 3.0 19.2 1.0 CG A:HIS34 3.0 21.0 1.0 CB A:CYS37 3.3 18.6 1.0 CB A:CYS11 3.3 16.3 1.0 CB A:CYS13 3.4 22.4 1.0 CB A:HIS34 3.4 17.5 1.0 NE2 A:HIS34 4.1 23.9 1.0 CD2 A:HIS34 4.2 22.6 1.0 N A:HIS34 4.3 18.8 1.0 N A:CYS13 4.3 21.4 1.0 CA A:HIS34 4.4 20.1 1.0 CA A:CYS13 4.4 22.2 1.0 OG1 A:THR15 4.6 23.9 1.0 CA A:CYS37 4.7 17.4 1.0 CA A:CYS11 4.7 18.8 1.0 N A:ILE12 4.8 20.8 1.0 N A:CYS37 5.0 18.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Bptf Phd-Bromodomain Module Bound to H3KC4ME3 Methyl Lysine Analog


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Bptf Phd-Bromodomain Module Bound to H3KC4ME3 Methyl Lysine Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:17.5 occ:1.00 SG A:CYS53 2.2 19.4 1.0 SG A:CYS56 2.2 15.8 1.0 SG A:CYS29 2.2 18.2 1.0 SG A:CYS26 2.4 16.8 1.0 CB A:CYS29 3.2 18.0 1.0 CB A:CYS56 3.2 19.3 1.0 CB A:CYS26 3.2 17.6 1.0 CB A:CYS53 3.4 19.2 1.0 N A:CYS29 3.7 17.5 1.0 OH A:TYR33 3.8 23.7 1.0 CA A:CYS29 4.0 21.2 1.0 N A:CYS53 4.1 15.5 1.0 O A:HOH386 4.2 19.7 1.0 CA A:CYS53 4.3 17.9 1.0 CE2 A:TYR33 4.3 20.1 1.0 CA A:CYS56 4.3 19.4 1.0 N A:CYS56 4.4 19.0 1.0 CZ A:TYR33 4.5 19.7 1.0 CB A:ARG28 4.6 18.6 1.0 CA A:CYS26 4.6 18.6 1.0 C A:ARG28 4.8 20.1 1.0 O A:CYS53 4.9 19.6 1.0 C A:CYS53 4.9 18.1 1.0 C A:CYS29 5.0 19.0 1.0

Z.Chen, A.J.Ruthenburg, R.Q.Notti, B.Ueberheide, L.A.Banaszynski. Quantitative and Structural Assessment of Methyllysine Analog Engagement By Cognate Binding Proteins Reveals Decrements That Can Impact Qualitative Experiment Interpretation To Be Published.